\HeaderA{calcGraphStats}{A function to calculate the various summary statistics for Y2H
induced graphs}{calcGraphStats}
\keyword{datagen}{calcGraphStats}
\begin{Description}\relax
This function takes a putative protein complex (given by comp) and a
list of bait to prey associations, and from these two data-sets
computes various summary statistics on the induced Y2H graph which
include: edge proportion of sampled nodes (baits to prey); estimated
population mean nodal degree; proportion of sampled baits with hits to
baits with no hits; the average out degree of baits; the proteins
(bait and prey) which are not isolated; the number of connected
components to the y2h graph, etc.
\end{Description}
\begin{Usage}
\begin{verbatim}
calcGraphStats(comp, bait2PreyL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{comp}] The \code{comp} argument is a character vector containing
the constituent proteins of some putative protein complex
\item[\code{bait2PreyL}] A named list of lists. Each name represents a
particular Y2H experiment; within each experimental entry, there is
two more lists: 1. bpList and 2. expList. bpList is a named list of
character vectors; each name corresponds to a bait protein of that
particular experiment, and the enry is a chracater vecotor of the
hit proteins found as prey. the expList is a named list concerning
experimental data: ActD gives the activation domain; GW is a logical
denoting if the prey list is genome wide; and numBaits details the
number of baits used in the experiment.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
For the bait2PreyL; use the the intactInfo.rda data-set of the package y2hStat.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{complex}] A character vector of the constituent members of the
proteinn complex of interest
\item[\code{complexBait}] A character vector of those protein members which
were also tested as baits in the y2h experiments
\item[\code{b2CompP}] A character vector of all proteins which were tested as
baits in the y2h experiments and also found a prey in the complex of
interest
\item[\code{notBait}] A character vector of those protein members which were
not tested as baits
\item[\code{avgDegOut}] The average out-degree of the bait proteins of the
complex of interest
\item[\code{notIsolated}] A character vector of proteins that showed
experimental binary affiliation for some other complex member
\item[\code{y2hGraph}] An instance of the class graph; a graphNEL induceds
Y2H graph on the protein complex
\item[\code{popMeanDegree}] The population mean degree derived from the
bait proteins
\item[\code{edgeProp}] The estimated edge proportions derived between
undirected Y2H edges
\item[\code{degBait}] A named list; each name corresponds to each member of
the protein complex with the entry the number of proteins to which
it is adjacent
\end{ldescription}
\end{Value}
\begin{Author}\relax
T Chiang
\end{Author}

